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Individual Residue Energy

Category: 
Scoring

Hi everyone,

I'm trying to get the energies of individual residues in a pose and am encountering an error that I can't seem to find much information on. Here is a sample of my script:

from pyrosetta import *
from pyrosetta.rosetta import *
from pyrosetta.rosetta.core.scoring import *

pyrosetta.init('-ignore_zero_occupancy false')

pose = pose_from_pdb(pdb_file)

sfxn = create_score_function('ref2015.wts')

score = pose.energies().residue_total_energy(1)

And here is the error I encounter:

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[Solved] Resetting a pose with RigidBodyTransMover

Category: 
Docking

I'm trying to seperate a protein-protein complex, apply residue labels based on core/surface/boundary layer definitions, and then reset the protein-protein complex for design. My first thought was to use the RigidBodyTransMover, however, I cannot perform the reverse rigid body translation to recombine the protein-protein complex; the ouput file has the proteins out of contact. I'm unfamiliar with the coordinates, but am noticing that the end coordinate differs after back transformation:

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Docking high and low resolution

Category: 
Docking

Hello,

 

I need to know about the method that is used for both high and low resolution docking. I know it is markov chain monte carlo, but I need to know in more details. Could you please provide me with a paper or any other resources about the method used for docking (in details)?

 

Thank you very much

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Assesing the docking

Category: 
Docking

Hello,

I followed the tutorial, and did docking. Now, I can see that the complex structure that I predicted is completely match the true complex structure. But, when I use TMalign and TMscore, they give me something like the following:

Name of Chain_1: predicted.pdb
Name of Chain_2: true.pdb
Length of Chain_1:  289 residues
Length of Chain_2:  579 residues

 

TM-score= 1.00000 (if normalized by length of Chain_1)
TM-score= 0.49914 (if normalized by length of Chain_2)

 

 

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where is generate_ligens.linuxgccrelease?

Category: 
Small Molecules

Hello, everyone!

I am reading Mr. Baker's paper titled "Computational design of ligand-binding proteins with high affinity and selectivity". In the supplementary data, they used generate_ligens.linuxiccrelease to generate ligand conformers. But I can't find generate_ligens tool in my directory (~/rosetta/bin), also I didn't find any record about it in Rosetta tutorials. Anyone konws where to find it?

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How do you combine two .pdb protein structure files of the same protein?

Category: 
Docking

I have a *.pdb file of one protein. I need to do protein protein docking for this protein (I have the original one and I will also make a duplicate of it). What is the best way to combine the original one and the duplicated in one pdb file (I'm doing this to prepare the final pdb for docking).

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